Contacts of the helix formed by residues 237 - 242 (chain D) in PDB entry 5YL4
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 237 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20D PHE* 3.8 13.8 - - + -
50D TYR* 3.5 27.4 - - - +
134D GLN* 4.2 6.7 - - - +
165D ASN* 6.0 0.9 - - - +
167D PHE* 4.4 6.7 - - + -
233D MET 3.1 20.8 + - - +
234D SER 3.4 2.6 + - - -
235D GLY 3.2 0.2 - - - -
236D VAL* 1.3 84.1 - - + +
238D THR* 1.3 58.5 + - - +
239D CYS 3.3 2.2 - - - -
240D LEU* 3.4 14.8 + - + -
241D ARG* 2.8 57.5 + - - +
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Residues in contact with THR 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234D SER 2.9 17.6 + - - -
235D GLY* 3.0 15.5 + - - -
237D THR* 1.3 75.8 - - - +
239D CYS* 1.3 60.5 + - - +
241D ARG* 3.7 6.4 + - - +
242D PHE* 3.1 37.6 + - + +
316D ILE* 4.3 10.8 - - + -
318D ARG* 3.4 29.0 + - + +
354D CYS* 3.8 37.2 - - + -
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Residues in contact with CYS 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D ARG* 3.3 16.8 + - - -
235D GLY 4.7 0.6 + - - -
236D VAL 5.3 3.1 - - - +
237D THR 3.3 0.4 - - - -
238D THR* 1.3 79.4 - - - +
240D LEU* 1.3 59.1 + - + +
242D PHE 3.5 7.9 - - - +
244D GLY* 5.4 2.7 + - - -
246D LEU* 3.7 18.5 - - - +
247D ASN* 3.5 28.5 - - + +
248D ALA* 3.7 9.3 - - - +
253D LEU* 6.3 0.2 - - + -
316D ILE* 3.5 34.3 - - + +
352D ALA* 4.2 16.4 - - - -
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Residues in contact with LEU 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D ILE* 3.8 26.9 - - + -
46D ARG* 3.4 21.2 + - - +
49D VAL* 3.6 18.3 - - + +
50D TYR* 4.1 11.2 - - + +
131D GLN* 4.3 4.3 - - - +
134D GLN* 5.1 1.1 - - - +
165D ASN* 5.8 1.3 - - - +
236D VAL 4.5 6.1 - - - +
237D THR* 3.4 24.1 + - + +
238D THR 3.3 0.4 - - - -
239D CYS* 1.3 76.9 - - + +
241D ARG* 1.3 61.0 + - + +
247D ASN 3.8 7.2 - - - +
248D ALA 3.4 22.4 - - - +
249D ASP* 3.6 24.5 - - - -
250D LEU* 3.8 19.3 - - + +
253D LEU* 5.8 6.1 - - + -
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Residues in contact with ARG 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D ILE* 3.6 27.1 - - - +
27D GLU* 3.2 20.8 + - - +
28D HIS* 3.4 50.9 + - + +
42D LEU 4.7 1.2 - - - +
46D ARG* 3.6 24.3 + - - +
49D VAL* 5.3 1.3 - - + -
50D TYR* 3.6 34.1 - - + -
234D SER* 2.7 43.2 + - - +
237D THR* 2.8 29.5 + - - +
238D THR* 3.4 9.1 + - - +
240D LEU* 1.3 78.6 - - - +
242D PHE* 1.3 76.0 + - + +
318D ARG* 4.1 0.2 - - - +
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Residues in contact with PHE 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D GLU* 4.1 19.5 - - + -
28D HIS* 3.9 21.3 - + - -
42D LEU* 3.5 33.0 - - + -
43D GLN* 4.4 6.5 - - + -
46D ARG* 4.0 10.4 + - - -
238D THR* 3.1 28.7 + - + +
239D CYS* 3.5 16.5 - - - +
241D ARG* 1.3 105.1 - - + +
243D PRO* 1.4 75.8 - - + +
244D GLY* 3.5 2.4 + - - -
318D ARG* 4.2 7.9 - - - -
354D CYS* 4.3 17.3 - - - -
356D ILE* 4.3 29.8 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il